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- PDB-4y00: Crystal Structure of Human TDP-43 RRM1 Domain with D169G Mutation... -

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Basic information

Entry
Database: PDB / ID: 4y00
TitleCrystal Structure of Human TDP-43 RRM1 Domain with D169G Mutation in Complex with an Unmodified Single-stranded DNA
Components
  • DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3')
  • TAR DNA-binding protein 43
KeywordsDNA BINDING PROTEIN/DNA / RNA recognition motif 1 Complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular membraneless organelle / negative regulation of protein phosphorylation / host-mediated suppression of viral transcription / pre-mRNA intronic binding / RNA splicing ...nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular membraneless organelle / negative regulation of protein phosphorylation / host-mediated suppression of viral transcription / pre-mRNA intronic binding / RNA splicing / response to endoplasmic reticulum stress / mRNA 3'-UTR binding / molecular condensate scaffold activity / positive regulation of insulin secretion / regulation of circadian rhythm / regulation of protein stability / positive regulation of protein import into nucleus / mRNA processing / cytoplasmic stress granule / rhythmic process / regulation of gene expression / double-stranded DNA binding / regulation of apoptotic process / amyloid fibril formation / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / lipid binding / chromatin / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
TAR DNA-binding protein 43, N-terminal / : / TAR DNA-binding protein 43, N-terminal domain / TAR DNA-binding protein 43, C-terminal / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...TAR DNA-binding protein 43, N-terminal / : / TAR DNA-binding protein 43, N-terminal domain / TAR DNA-binding protein 43, C-terminal / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / TAR DNA-binding protein 43
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChiang, C.H. / Kuo, P.H. / Yang, W.Z. / Yuan, H.S.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica, Taiwan, R.O.C. Taiwan
National Science Council, Taiwan, R.O.C. Taiwan
CitationJournal: Sci Rep / Year: 2016
Title: Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation
Authors: Chiang, C.H. / Grauffel, C. / Wu, L.S. / Kuo, P.H. / Doudeva, L.G. / Lim, C. / Shen, C.K. / Yuan, H.S.
History
DepositionFeb 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Oct 4, 2017Group: Derived calculations / Experimental preparation / Category: exptl_crystal_grow / pdbx_struct_oper_list
Item: _exptl_crystal_grow.pdbx_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAR DNA-binding protein 43
B: TAR DNA-binding protein 43
C: TAR DNA-binding protein 43
D: TAR DNA-binding protein 43
E: DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3')
F: DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3')
G: DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3')
H: DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)60,3918
Polymers60,3918
Non-polymers00
Water43224
1
A: TAR DNA-binding protein 43
E: DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)15,0982
Polymers15,0982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TAR DNA-binding protein 43
F: DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)15,0982
Polymers15,0982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TAR DNA-binding protein 43
G: DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)15,0982
Polymers15,0982
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TAR DNA-binding protein 43
H: DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)15,0982
Polymers15,0982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.636, 97.636, 96.871
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
TAR DNA-binding protein 43 / TDP-43


Mass: 12006.710 Da / Num. of mol.: 4 / Fragment: UNP residues 101-191 / Mutation: D169G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TARDBP, TDP43 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13148
#2: DNA chain
DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3')


Mass: 3091.026 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M CH3COONH4, pH 5.0, 15% v/v Jeffamine ED-2001, pH 7.0
PH range: 5.0-7.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 4, 2014
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→16.85 Å / Num. all: 11934 / Num. obs: 10669 / % possible obs: 97.86 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.061 / Rsym value: 0.049 / Net I/σ(I): 18.05
Reflection shellResolution: 2.899→3.003 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.5085 / Mean I/σ(I) obs: 5.96 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IUF

4iuf


Resolution: 3→16.847 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.77 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2949 1065 9.98 %
Rwork0.2658 --
obs0.2746 10669 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→16.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 495 0 24 3031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033120
X-RAY DIFFRACTIONf_angle_d0.6184293
X-RAY DIFFRACTIONf_dihedral_angle_d17.9291179
X-RAY DIFFRACTIONf_chiral_restr0.038469
X-RAY DIFFRACTIONf_plane_restr0.002450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0012-3.13690.48931370.44621224X-RAY DIFFRACTION90
3.1369-3.3010.44651270.39391182X-RAY DIFFRACTION89
3.301-3.50580.37681270.35831201X-RAY DIFFRACTION88
3.5058-3.77340.40991290.30141178X-RAY DIFFRACTION87
3.7734-4.14740.27261310.27011172X-RAY DIFFRACTION86
4.1474-4.73460.25791250.24111196X-RAY DIFFRACTION87
4.7346-5.9170.25221350.23091195X-RAY DIFFRACTION87
5.917-16.27290.24661400.21841252X-RAY DIFFRACTION86

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